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Sample GSM6265560 Query DataSets for GSM6265560
Status Public on Jun 24, 2022
Title I_SAIL_232 H3K4me3_ChIP-seq
Sample type SRA
Source name de-etiolated seedling
Organism Arabidopsis thaliana
Characteristics t-dna mutant: SAIL_232
antibodies: H3K4me3 (EMD Millipore, 04-745)
Treatment protocol no treatment
Growth protocol Seedlings were grown on Linsmaier and Skoog medium supplemented with 1% sucrose, sample 12 is derived from flowers of soil-grown plants
Extracted molecule genomic DNA
Extraction protocol Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
Description Histone modification
Data processing base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
ChIP-seq peak identification with SICER 1.1 with the following setting: redundancy threshold (1), window size (200), fragment size (100), effective genome fraction (0.8), gap size (600), FDR (0.01)
Genome_build: TAIR10
Submission date Jun 23, 2022
Last update date Nov 29, 2022
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platform ID GPL21785
Series (1)
GSE108401 The Complex Architecture of Transgene Insertions
BioSample SAMN29271684
SRA SRX15855496

Supplementary file Size Download File type/resource 19.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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